2 C Read the PDB file and convert the peptide geometry into virtual-chain
6 include 'DIMENSIONS.FREE'
7 include 'DIMENSIONS.ZSCOPT'
8 include 'COMMON.CONTROL'
11 include 'COMMON.CHAIN'
12 include 'COMMON.INTERACT'
13 include 'COMMON.IOUNITS'
15 include 'COMMON.NAMES'
16 character*3 seq,atom,res
18 double precision sccor(3,20)
19 integer i,j,iii,ibeg,ishift,ishift1,ity,ires,ires_old
21 integer rescode,kkk,lll,icha,cou,kupa,iprzes
25 read (ipdbin,'(a80)',end=10) card
26 if (card(:3).eq.'END') then
28 else if (card(:3).eq.'TER') then
32 itype(ires_old-1)=ntyp1
35 c write (iout,*) "Chain ended",ires,ishift,ires_old
36 call sccenter(ires,iii,sccor)
38 C Fish out the ATOM cards.
39 if (index(card(1:4),'ATOM').gt.0) then
40 read (card(14:16),'(a3)') atom
41 if (atom.eq.'CA' .or. atom.eq.'CH3') then
42 C Calculate the CM of the preceding residue.
44 call sccenter(ires,iii,sccor)
47 c write (iout,'(a80)') card
48 read (card(24:26),*) ires
49 read (card(18:20),'(a3)') res
52 if (res.ne.'GLY' .and. res.ne. 'ACE') then
56 c write (iout,*) "ires",ires," ibeg",ibeg," ishift",ishift
58 else if (ibeg.eq.2) then
60 ishift=-ires_old+ires-1
61 c write (iout,*) "New chain started",ires,ishift
65 c write (2,*) "ires",ires," ishift",ishift
66 if (res.eq.'ACE') then
69 itype(ires)=rescode(ires,res,0)
71 read(card(31:54),'(3f8.3)') (c(j,ires),j=1,3)
72 write (iout,'(2i3,2x,a,3f8.3)')
73 & ires,itype(ires),res,(c(j,ires),j=1,3)
76 sccor(j,iii)=c(j,ires)
78 else if (atom.ne.'O '.and.atom(1:1).ne.'H' .and.
79 & atom.ne.'N ' .and. atom.ne.'C ') then
81 read(card(31:54),'(3f8.3)') (sccor(j,iii),j=1,3)
85 10 write (iout,'(a,i5)') ' Nres: ',ires
86 C Calculate dummy residue coordinates inside the "chain" of a multichain
90 c write (iout,*) i,itype(i)
92 if (itype(i).eq.ntyp1) then
93 if (itype(i+1).eq.ntyp1) then
94 C 16/01/2014 by Adasko: Adding to dummy atoms in the chain
95 C first is connected prevous chain (itype(i+1).eq.ntyp1)=true
96 C second dummy atom is conected to next chain itype(i+1).eq.ntyp1=false
98 C 2/15/2013 by Adam: corrected insertion of the last dummy residue
99 C call refsys(i-3,i-2,i-1,e1,e2,e3,fail)
106 C c(j,i)=c(j,i-1)-1.9d0*e2(j)
110 dcj=(c(j,i-2)-c(j,i-3))/2.0
115 else !itype(i+1).eq.ntyp1
116 C if (unres_pdb) then
117 C 2/15/2013 by Adam: corrected insertion of the first dummy residue
118 C call refsys(i+1,i+2,i+3,e1,e2,e3,fail)
125 C c(j,i)=c(j,i+1)-1.9d0*e2(j)
129 dcj=(c(j,i+3)-c(j,i+2))/2.0
134 endif !itype(i+1).eq.ntyp1
135 endif !itype.eq.ntyp1
137 C Calculate the CM of the last side chain.
138 call sccenter(ires,iii,sccor)
141 if (itype(nres).ne.10) then
145 dcj=(c(j,nres-2)-c(j,nres-3))/2.0
146 c(j,nres)=c(j,nres-1)+dcj
147 c(j,2*nres)=c(j,nres)
157 c(j,2*nres)=c(j,nres)
159 if (itype(1).eq.ntyp1) then
163 dcj=(c(j,4)-c(j,3))/2.0
168 C Calculate internal coordinates.
170 write (iout,'(2i3,2x,a,3f8.3,5x,3f8.3)')
171 & ires,itype(ires),restyp(itype(ires)),(c(j,ires),j=1,3),
172 & (c(j,nres+ires),j=1,3)
174 call int_from_cart1(.false.)
175 call int_from_cart(.true.,.false.)
176 call sc_loc_geom(.true.)
177 write (iout,*) "After int_from_cart"
181 dc(j,i)=c(j,i+1)-c(j,i)
182 dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
187 dc(j,i+nres)=c(j,i+nres)-c(j,i)
188 dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
190 c write (iout,*) i,(dc(j,i+nres),j=1,3),(dc_norm(j,i+nres),j=1,3),
198 theta_ref(i)=theta(i)
204 C Copy the coordinates to reference coordinates
210 C Splits to single chain if occurs
216 cc write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
218 if ((itype(i-1).eq.ntyp1).and.(i.gt.2).and.(i.ne.nres)) then
221 c write (iout,*) "spraw lancuchy",(c(j,i),j=1,3)
227 cref(j,i+nres,cou)=c(j,i+nres)
229 chain_rep(j,lll,kkk)=c(j,i)
230 chain_rep(j,lll+nres,kkk)=c(j,i+nres)
234 if (chain_length.eq.0) chain_length=nres
235 write (iout,*) chain_length
237 chain_rep(j,chain_length,symetr)=chain_rep(j,chain_length,1)
238 chain_rep(j,chain_length+nres,symetr)
239 &=chain_rep(j,chain_length+nres,1)
244 c write (iout,*) "spraw lancuchy",chain_length,symetr
246 c do kkk=1,chain_length
247 c write (iout,*) itype(kkk),(chain_rep(j,kkk,i), j=1,3)
251 C makes copy of chains
252 c write (iout,*) "symetr", symetr
254 if (symetr.gt.1) then
261 c write(iout,*) "tabperm", (tabperm(i,kkk),kkk=1,4)
267 c write (iout,*) i,icha
268 do lll=1,chain_length
270 if (cou.le.nres) then
272 kupa=mod(lll,chain_length)
273 iprzes=(kkk-1)*chain_length+lll
274 if (kupa.eq.0) kupa=chain_length
275 c write (iout,*) "kupa", kupa
276 cref(j,iprzes,i)=chain_rep(j,kupa,icha)
277 cref(j,iprzes+nres,i)=chain_rep(j,kupa+nres,icha)
284 C-koniec robienia kopidm
286 write (iout,*) "nowa struktura", nperm
288 write (iout,110) restyp(itype(i)),i,cref(1,i,kkk),
290 &cref(3,i,kkk),cref(1,nres+i,kkk),
291 &cref(2,nres+i,kkk),cref(3,nres+i,kkk)
293 100 format (//' alpha-carbon coordinates ',
294 & ' centroid coordinates'/
295 1 ' ', 6X,'X',11X,'Y',11X,'Z',
296 & 10X,'X',11X,'Y',11X,'Z')
297 110 format (a,'(',i3,')',6f12.5)
304 c---------------------------------------------------------------------------
305 subroutine int_from_cart(lside,lprn)
308 include 'DIMENSIONS.ZSCOPT'
309 include 'COMMON.LOCAL'
311 include 'COMMON.CHAIN'
312 include 'COMMON.INTERACT'
313 include 'COMMON.IOUNITS'
315 include 'COMMON.NAMES'
316 character*3 seq,atom,res
318 double precision sccor(3,20)
320 double precision dist,alpha,beta,di
325 & 'Internal coordinates calculated from crystal structure.'
327 write (iout,'(8a)') ' Res ',' dvb',' Theta',
328 & ' Phi',' Dsc_id',' Dsc',' Alpha',
331 write (iout,'(4a)') ' Res ',' dvb',' Theta',
337 if (iti.ne.ntyp1 .and. itype(i+1).ne.ntyp1 .and.
338 & (dist(i,i+1).lt.2.0D0 .or. dist(i,i+1).gt.5.0D0)) then
339 write (iout,'(a,i4)') 'Bad Cartesians for residue',i
342 vbld(i+1)=dist(i,i+1)
343 vbld_inv(i+1)=1.0d0/vbld(i+1)
344 if (i.gt.1) theta(i+1)=alpha(i-1,i,i+1)
345 if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
350 c(j,maxres2)=0.5D0*(c(j,i-1)+c(j,i+1))
355 alph(i)=alpha(nres+i,i,maxres2)
356 omeg(i)=beta(nres+i,i,maxres2,i+1)
359 & write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
360 & rad2deg*theta(i),rad2deg*phi(i),dsc(iti),di,
361 & rad2deg*alph(i),rad2deg*omeg(i)
366 write (iout,'(a3,i4,7f10.3)') restyp(iti),i,dist(i,i-1),
367 & rad2deg*theta(i),rad2deg*phi(i)
373 c-------------------------------------------------------------------------------
374 subroutine sc_loc_geom(lprn)
375 implicit real*8 (a-h,o-z)
377 include 'DIMENSIONS.ZSCOPT'
378 include 'DIMENSIONS.FREE'
379 include 'COMMON.LOCAL'
381 include 'COMMON.CHAIN'
382 include 'COMMON.INTERACT'
383 include 'COMMON.IOUNITS'
385 include 'COMMON.NAMES'
386 include 'COMMON.CONTROL'
387 include 'COMMON.SETUP'
388 double precision x_prime(3),y_prime(3),z_prime(3)
392 dc_norm(j,i)=vbld_inv(i+1)*(c(j,i+1)-c(j,i))
396 if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
398 dc_norm(j,i+nres)=vbld_inv(i+nres)*(c(j,i+nres)-c(j,i))
402 dc_norm(j,i+nres)=0.0d0
407 costtab(i+1) =dcos(theta(i+1))
408 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
409 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
410 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
411 cosfac2=0.5d0/(1.0d0+costtab(i+1))
412 cosfac=dsqrt(cosfac2)
413 sinfac2=0.5d0/(1.0d0-costtab(i+1))
414 sinfac=dsqrt(sinfac2)
416 if (it.ne.10 .and. itype(i).ne.ntyp1) then
418 C Compute the axes of tghe local cartesian coordinates system; store in
419 c x_prime, y_prime and z_prime
427 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
428 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
430 call vecpr(x_prime,y_prime,z_prime)
432 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
433 C to local coordinate system. Store in xx, yy, zz.
439 xx = xx + x_prime(j)*dc_norm(j,i+nres)
440 yy = yy + y_prime(j)*dc_norm(j,i+nres)
441 zz = zz + z_prime(j)*dc_norm(j,i+nres)
456 if(me.eq.king.or..not.out1file)
457 & write (iout,'(a3,i4,3f10.5)') restyp(iti),i,xxref(i),
463 c---------------------------------------------------------------------------
464 subroutine sccenter(ires,nscat,sccor)
467 include 'COMMON.CHAIN'
468 integer ires,nscat,i,j
469 double precision sccor(3,20),sccmj
473 sccmj=sccmj+sccor(j,i)
475 dc(j,ires)=sccmj/nscat